scholarly journals DNA Oligomers Containing Site-Specific and Stereospecific Exocyclic Deoxyadenosine Adducts of 1,2,3,4-Diepoxybutane: Synthesis, Characterization, and Effects on DNA Structure

2010 ◽  
Vol 23 (10) ◽  
pp. 1556-1567 ◽  
Author(s):  
Uthpala Seneviratne ◽  
Sergey Antsypovich ◽  
Danae Quirk Dorr ◽  
Thakshila Dissanayake ◽  
Srikanth Kotapati ◽  
...  
Keyword(s):  
Dna Structure ◽  
Dna Oligomers ◽  
Site Specific ◽  
Deoxyadenosine Adducts

Selective Functionalization at N2-Position of Guanine in Oligonucleotides via Reductive Amination

2020 ◽  
Author(s):  
Bapurao Bhoge ◽  
Ishu Saraogi
Keyword(s):  
Organic Chemistry ◽  
Chemical Biology ◽  
Reductive Amination ◽  
The Other ◽  
Dna Oligomers ◽  
Site Specific ◽  
Wide Applicability ◽  
Dna Oligonucleotides ◽  
Selective Functionalization

Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. Here we have employed a classical reaction in organic chemistry, reductive amination, to selectively functionalize the N<sup>2</sup>-amine of guanine/2’-deoxyguanine monophosphate. This method specifically modifies guanine in several tested DNA oligonucleotides, while leaving the other bases unaffected. Using this approach, we have successfully incorporated desired handles chemoselectively into DNA oligomers.

Sequence Context Effects on Mutational Properties of cis-Opened Benzo[c]phenanthrene Diol Epoxide−Deoxyadenosine Adducts in Site-Specific Mutation Studies†

Biochemistry ◽  
1999 ◽  
Vol 38 (3) ◽  
pp. 1144-1152 ◽  
Author(s):  
Ingrid Pontén ◽  
Jane M. Sayer ◽  
Anthony S. Pilcher ◽  
Haruhiko Yagi ◽  
Subodh Kumar ◽  
...  
Keyword(s):  
Context Effects ◽  
Sequence Context ◽  
Site Specific ◽  
Specific Mutation ◽  
Diol Epoxide ◽  
Deoxyadenosine Adducts

DNA ORIGAMI SITE-SPECIFIC ARRANGEMENT OF GOLD NANOPARTICLES

NANO ◽  
2013 ◽  
Vol 08 (06) ◽  
pp. 1350064
Author(s):  
AMOAKO GEORGE ◽  
RIAN YE ◽  
LIZHOU ZHUANG ◽  
XIAOHONG YANG ◽  
ZHIYONG SHEN ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Gel Electrophoresis ◽  
Dna Origami ◽  
Covalent Attachment ◽  
Agarose Gel Electrophoresis ◽  
Dna Oligomers ◽  
Site Specific ◽  
Modified Dna ◽  
Vis Spectroscopy ◽  
Potential Use

Controlling matter at the nanoscale holds a lot of promise in nanotechnology. The DNA origami is promising if used as a template to design and arrange matter at the nanoscale. We have used the DNA origami approach to engineer staple strands at selected sites for attachment of gold nanoparticles. The covalent attachment of thiol-modified DNA oligomers was used to functionalize gold nanoparticles. These oligomers then hybridize with complementary strands extended on selected staple strands on the DNA origami surface with nanometer precision. Gold nanoparticles of 5 nm diameter were arranged across a DNA origami tube to form a C -shape which has potential use in electronics and plasmonics. Agarose gel electrophoresis, AFM, UV-Vis spectroscopy and TEM were used to characterize the structure.

Site-specific polymerase incorporation of consecutive ligand-containing nucleotides for multiple metal-mediated base pairing

2021 ◽  
Author(s):  
Takahiro Nakama ◽  
Yusuke Takezawa ◽  
Mitsuhiko Shionoya
Keyword(s):  
Enzymatic Method ◽  
Base Pairing ◽  
Base Pairs ◽  
Dna Oligomers ◽  
Site Specific ◽  
Ligand Type

An enzymatic method has been developed for the synthesis of DNA oligomers containing consecutive artificial ligand-type nucleotides. Three hydroxypyridone ligand-containing nucleotides forming CuII-mediated unnatural base pairs were continuously incorporated at...

scholarly journals Selective Functionalization at N2-Position of Guanine in Oligonucleotides via Reductive Amination

2020 ◽  
Author(s):  
Bapurao Bhoge ◽  
Ishu Saraogi
Keyword(s):  
Organic Chemistry ◽  
Chemical Biology ◽  
Reductive Amination ◽  
The Other ◽  
Dna Oligomers ◽  
Site Specific ◽  
Wide Applicability ◽  
Dna Oligonucleotides ◽  
Selective Functionalization

Chemo- and site-specific modifications in oligonucleotides have wide applicability as mechanistic probes in chemical biology. Here we have employed a classical reaction in organic chemistry, reductive amination, to selectively functionalize the N<sup>2</sup>-amine of guanine/2’-deoxyguanine monophosphate. This method specifically modifies guanine in several tested DNA oligonucleotides, while leaving the other bases unaffected. Using this approach, we have successfully incorporated desired handles chemoselectively into DNA oligomers.

scholarly journals Thymidine Glycol: The Effect on DNA Structure and DNA Binding by Site-Specific Proteins

2015 ◽  
Vol 07 (11) ◽  
pp. 491-509
Author(s):  
Elena A. Kubareva ◽  
Fan Yang ◽  
Alexandra Yu. Ryazanova ◽  
Nina G. Dolinnaya ◽  
Andrei V. Golovin ◽  
...  
Keyword(s):  
Dna Binding ◽  
Dna Structure ◽  
Site Specific ◽  
Specific Proteins ◽  
Thymidine Glycol

Large-cluster and combined fluorescent and gold immunoprobes

1996 ◽  
Vol 54 ◽  
pp. 892-893
Author(s):  
Richard D. Powell ◽  
James F. Hainfeld ◽  
Carol M. R. Halsey ◽  
David L. Spector ◽  
Shelley Kaurin ◽  
...  
Keyword(s):  
Metal Cluster ◽  
Sulfonyl Chloride ◽  
Gel Filtration ◽  
Cross Linking ◽  
Site Specific ◽  
Fab Fragments ◽  
Cluster Label ◽  
Covalently Linked ◽  
Texas Red ◽  
Fold Excess

Two new types of covalently linked, site-specific immunoprobes have been prepared using metal cluster labels, and used to stain components of cells. Combined fluorescein and 1.4 nm “Nanogold” labels were prepared by using the fluorescein-conjugated tris (aryl) phosphine ligand and the amino-substituted ligand in the synthesis of the Nanogold cluster. This cluster label was activated by reaction with a 60-fold excess of (sulfo-Succinimidyl-4-N-maleiniido-cyclohexane-l-carboxylate (sulfo-SMCC) at pH 7.5, separated from excess cross-linking reagent by gel filtration, and mixed in ten-fold excess with Goat Fab’ fragments against mouse IgG (obtained by reduction of F(ab’)2 fragments with 50 mM mercaptoethylamine hydrochloride). Labeled Fab’ fragments were isolated by gel filtration HPLC (Superose-12, Pharmacia). A combined Nanogold and Texas Red label was also prepared, using a Nanogold cluster derivatized with both and its protected analog: the cluster was reacted with an eight-fold excess of Texas Red sulfonyl chloride at pH 9.0, separated from excess Texas Red by gel filtration, then deprotected with HC1 in methanol to yield the amino-substituted label.

The challenge of detecting modifications on proteins

2020 ◽  
Vol 64 (1) ◽  
pp. 135-153 ◽  
Author(s):  
Lauren Elizabeth Smith ◽  
Adelina Rogowska-Wrzesinska
Keyword(s):  
Mass Spectrometry ◽  
Protein Function ◽  
Chemical Properties ◽  
Lysine Acetylation ◽  
Mass Determination ◽  
Post Translational Modifications ◽  
Site Specific ◽  
The Common

Abstract Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.

Sign in / Sign up

Export Citation Format

Share Document